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{{short description|Type of microorganism that produces methane as a waste product}}
{{Distinguish|Methanotroph}}
Methanogens are anaerobic archaea that produce [[methane]] as a byproduct of their energy metabolism, i.e., [[catabolism]]. Methane production, or [[methanogenesis]], is the only biochemical pathway for [[Adenosine triphosphate|ATP]] generation in methanogens. All known methanogens belong exclusively to the domain [[Archaea]], although some bacteria, plants, and animal cells are also known to produce methane.<ref>{{Cite journal |last1=Ernst |first1=Leonard |last2=Steinfeld |first2=Benedikt |last3=Barayeu |first3=Uladzimir |last4=Klintzsch |first4=Thomas |last5=Kurth |first5=Markus |last6=Grimm |first6=Dirk |last7=Dick |first7=Tobias P. |last8=Rebelein |first8=Johannes G. |last9=Bischofs |first9=Ilka B. |last10=Keppler |first10=Frank |date=2022-03-17 |title=Methane formation driven by reactive oxygen species across all living organisms |url=https://www.nature.com/articles/s41586-022-04511-9 |journal=Nature |language=en |volume=603 |issue=7901 |pages=482–487 |doi=10.1038/s41586-022-04511-9 |pmid=35264795 |bibcode=2022Natur.603..482E |issn=0028-0836}}</ref> However, the biochemical pathway for methane production in these organisms differs from that in methanogens and does not contribute to ATP formation. Methanogens belong to various [[Phylum|phyla]] within the domain Archaea. Previous studies placed all known methanogens into the superphylum Euryarchaeota.<ref>{{Cite journal |last1=Liu |first1=Yuchen |last2=Whitman |first2=William B. |date=March 2008 |title=Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea |url=https://nyaspubs.onlinelibrary.wiley.com/doi/10.1196/annals.1419.019 |journal=Annals of the New York Academy of Sciences |language=en |volume=1125 |issue=1 |pages=171–189 |doi=10.1196/annals.1419.019 |pmid=18378594 |bibcode=2008NYASA1125..171L |issn=0077-8923}}</ref><ref name=":0" /> However, recent phylogenomic data have led to their reclassification into several different phyla.<ref name=":1">{{cite web |title=Archived copy |url=http://spacecenter.uark.edu/JillJabstract.doc |url-status=dead |archive-url=https://web.archive.org/web/20090327135553/http://spacecenter.uark.edu/JillJabstract.doc |archive-date=2009-03-27 |access-date=2009-09-20}}</ref> Methanogens are common in various anoxic environments, such as marine and freshwater sediments, wetlands, the digestive tracts of animals, wastewater treatment plants, rice paddy soil, and landfills.<ref name=":2" /> While some methanogens are extremophiles, such as ''Methanopyrus kandleri'', which grows between 84 and 110°C,<ref name=":3" /> or ''Methanonatronarchaeum thermophilum'', which grows at a pH range of 8.2 to 10.2 and a Na+ concentration of 3 to 4.8 M,<ref name=":4" /> most of the isolates are mesophilic and grow around neutral pH.<ref name=":5" />
==Physical description==
Methanogens are usually cocci (spherical) or rods (cylindrical) in shape, but long filaments (''Methanobrevibacter filliformis'', ''Methanospirillum hungatei'') and curved forms (''Methanobrevibacter curvatus'', ''Methanobrevibacter cuticularis'') also occur. There are over 150 described species of methanogens,<ref>{{Cite web |title=Leibniz Institute DSMZ: Welcome to the Leibniz Institute DSMZ |url=https://www.dsmz.de/ |access-date=2024-07-17 |website=www.dsmz.de |language=en-US}}</ref> which do not form a [[monophyletic]] group in the phylum [[Euryarchaeota]] (see Taxonomy). They are exclusively anaerobic organisms that cannot function under aerobic conditions due to the extreme oxygen sensitivity of methanogenesis enzymes and FeS clusters involved in ATP production. However, the degree of oxygen sensitivity varies, as methanogenesis has often been detected in temporarily oxygenated environments such as rice paddy soil,<ref>{{Cite journal |last1=Angel |first1=Roey |last2=Matthies |first2=Diethart |last3=Conrad |first3=Ralf |date=2011-05-31 |title=Activation of Methanogenesis in Arid Biological Soil Crusts Despite the Presence of Oxygen |journal=PLOS ONE |volume=6 |issue=5 |pages=e20453 |doi=10.1371/journal.pone.0020453 |doi-access=free |pmid=21655270 |pmc=3105065 |bibcode=2011PLoSO...620453A |issn=1932-6203}}</ref><ref>{{Cite journal |last1=Angel |first1=Roey |last2=Claus |first2=Peter |last3=Conrad |first3=Ralf |date=April 2012 |title=Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions |journal=The ISME Journal |language=en |volume=6 |issue=4 |pages=847–862 |doi=10.1038/ismej.2011.141 |issn=1751-7362 |pmc=3309352 |pmid=22071343|bibcode=2012ISMEJ...6..847A }}</ref><ref>{{Cite journal |last=Conrad |first=Ralf |date=2020-06-11 |title=Methane Production in Soil Environments—Anaerobic Biogeochemistry and Microbial Life between Flooding and Desiccation |journal=Microorganisms |volume=8 |issue=6 |pages=881 |doi=10.3390/microorganisms8060881 |doi-access=free |pmid=32545191 |pmc=7357154 |issn=2076-2607}}</ref> and various molecular mechanisms potentially involved in oxygen and [[reactive oxygen species]] (ROS) detoxification have been proposed.<ref>{{Cite journal |last1=Lyu |first1=Zhe |last2=Lu |first2=Yahai |date=2017-11-14 |title=Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments |url=http://dx.doi.org/10.1038/ismej.2017.173 |journal=The ISME Journal |volume=12 |issue=2 |pages=411–423 |doi=10.1038/ismej.2017.173 |pmid=29135970 |pmc=5776455 |bibcode=2018ISMEJ..12..411L |issn=1751-7362}}</ref> For instance, a recently identified species Candidatus Methanothrix paradoxum common in wetlands and soil can function in anoxic microsites within aerobic environments<ref>{{Cite journal |last1=Angle |first1=Jordan C. |last2=Morin |first2=Timothy H. |last3=Solden |first3=Lindsey M. |last4=Narrowe |first4=Adrienne B. |last5=Smith |first5=Garrett J. |last6=Borton |first6=Mikayla A. |last7=Rey-Sanchez |first7=Camilo |last8=Daly |first8=Rebecca A. |last9=Mirfenderesgi |first9=Golnazalsdat |last10=Hoyt |first10=David W. |last11=Riley |first11=William J. |last12=Miller |first12=Christopher S. |last13=Bohrer |first13=Gil |last14=Wrighton |first14=Kelly C. |date=2017-11-16 |title=Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions |url=http://dx.doi.org/10.1038/s41467-017-01753-4 |journal=Nature Communications |volume=8 |issue=1 |page=1567 |doi=10.1038/s41467-017-01753-4 |pmid=29146959 |pmc=5691036 |bibcode=2017NatCo...8.1567A |issn=2041-1723}}</ref> but it is sensitive to the presence of [[oxygen]] even at trace level and cannot usually sustain oxygen stress for a prolonged time. However, ''[[Methanosarcina barkeri]]'' from a sister family ''Methanosarcinaceae'' is exceptional in possessing a [[superoxide dismutase]] (SOD) [[enzyme]], and may survive longer than the others in the presence of O<sub>2</sub>.<ref name=":0">{{cite journal |last1=Peters |first1=V. |last2=Conrad |first2=R. |date=1995 |title=Methanogenic and other strictly anaerobic bacteria in desert soil and other oxic sois |journal=Applied and Environmental Microbiology |volume=61 |issue=4 |pages=1673–1676|doi=10.1128/AEM.61.4.1673-1676.1995 |pmid=16535011 |pmc=1388429 |bibcode=1995ApEnM..61.1673P }}</ref>
As is the case for other archaea, methanogens lack [[peptidoglycan]], a polymer that is found in the [[cell wall]]s of [[bacteria]].<ref>{{Cite journal |last1=van Wolferen |first1=Marleen |last2=Pulschen |first2=Andre Arashiro |last3=Baum |first3=Buzz |last4=Gribaldo |first4=Simonetta |last5=Albers |first5=Sonja-Verena |date=2022-10-17 |title=The cell biology of archaea |journal=Nature Microbiology |language=en |volume=7 |issue=11 |pages=1744–1755 |doi=10.1038/s41564-022-01215-8 |issn=2058-5276 |pmc=7613921 |pmid=36253512}}</ref> Instead, some methanogens have a cell wall formed by [[pseudopeptidoglycan]] (also known as [[pseudomurein]]). Other methanogens have a [[paracrystalline]] protein array (S-layer) that fit together like a [[jigsaw puzzle]].<ref name=":2">{{Cite book|title=Bergey's Manual of Systematics of Archaea and Bacteria|pages = 1–8|last=Boone|first=David R.|date=2015|publisher=John Wiley & Sons, Ltd|isbn=9781118960608|language=en|doi=10.1002/9781118960608.gbm00495|chapter = Methanobacterium}}</ref> In some lineages there are less common types of cell envelope such as proteinaceous sheath of ''Methanospirillum'' or methanochondroitin of ''Methanosarcina'' aggregated cells.<ref>{{Cite journal |last1=Albers |first1=Sonja-Verena |last2=Meyer |first2=Benjamin H. |date=June 2011 |title=The archaeal cell envelope |url=https://www.nature.com/articles/nrmicro2576 |journal=Nature Reviews Microbiology |language=en |volume=9 |issue=6 |pages=414–426 |doi=10.1038/nrmicro2576 |pmid=21572458 |issn=1740-1526}}</ref>
==Ecology==
In [[Hypoxia (environmental)|anaerobic environments]], methanogens play a vital ecological role, removing excess hydrogen and fermentation products that have been produced by other forms of [[anaerobic respiration]].<ref>{{Cite journal |last1=Thauer |first1=Rudolf K. |last2=Kaster |first2=Anne-Kristin |last3=Seedorf |first3=Henning |last4=Buckel |first4=Wolfgang |last5=Hedderich |first5=Reiner |date=August 2008 |title=Methanogenic archaea: ecologically relevant differences in energy conservation |url=https://www.nature.com/articles/nrmicro1931 |journal=Nature Reviews Microbiology |language=en |volume=6 |issue=8 |pages=579–591 |doi=10.1038/nrmicro1931 |pmid=18587410 |issn=1740-1526}}</ref> Methanogens typically thrive in environments in which all [[electron acceptor]]s other than CO<sub>2</sub> (such as [[oxygen]], [[nitrate]], ferric [[iron]] (Fe(III)), and [[sulfate]]) have been depleted. Such environments include wetlands and rice paddy soil, the digestive tracts of various animals (ruminants, arthropods, humans),<ref>{{Cite journal |last1=Chibani |first1=Cynthia Maria |last2=Mahnert |first2=Alexander |last3=Borrel |first3=Guillaume |last4=Almeida |first4=Alexandre |last5=Werner |first5=Almut |last6=Brugère |first6=Jean-François |last7=Gribaldo |first7=Simonetta |last8=Finn |first8=Robert D. |last9=Schmitz |first9=Ruth A. |last10=Moissl-Eichinger |first10=Christine |date=2021-12-30 |title=A catalogue of 1,167 genomes from the human gut archaeome |journal=Nature Microbiology |language=en |volume=7 |issue=1 |pages=48–61 |doi=10.1038/s41564-021-01020-9 |issn=2058-5276 |pmc=8727293 |pmid=34969981}}</ref><ref>{{Cite journal |last1=Protasov |first1=Evgenii |last2=Nonoh |first2=James O. |last3=Kästle Silva |first3=Joana M. |last4=Mies |first4=Undine S. |last5=Hervé |first5=Vincent |last6=Dietrich |first6=Carsten |last7=Lang |first7=Kristina |last8=Mikulski |first8=Lena |last9=Platt |first9=Katja |last10=Poehlein |first10=Anja |last11=Köhler-Ramm |first11=Tim |last12=Miambi |first12=Edouard |last13=Boga |first13=Hamadi I. |last14=Feldewert |first14=Christopher |last15=Ngugi |first15=David K. |date=2023-11-15 |title=Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods |journal=Frontiers in Microbiology |volume=14 |doi=10.3389/fmicb.2023.1281628 |doi-access=free |issn=1664-302X |pmc=10684969 |pmid=38033561}}</ref><ref>{{Cite journal |last1=Thomas |first1=Courtney M. |last2=Desmond-Le Quéméner |first2=Elie |last3=Gribaldo |first3=Simonetta |last4=Borrel |first4=Guillaume |date=2022-06-10 |title=Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom |url=http://dx.doi.org/10.1038/s41467-022-31038-4 |journal=Nature Communications |volume=13 |issue=1 |page=3358 |doi=10.1038/s41467-022-31038-4 |pmid=35688919 |bibcode=2022NatCo..13.3358T |issn=2041-1723|pmc=9187648 }}</ref> wastewater treatment plants and landfills, deep-water oceanic sediments, and hydrothermal vents.<ref>{{Cite journal |last1=Lyu |first1=Zhe |last2=Shao |first2=Nana |last3=Akinyemi |first3=Taiwo |last4=Whitman |first4=William B. |date=July 2018 |title=Methanogenesis |url=https://linkinghub.elsevier.com/retrieve/pii/S0960982218306237 |journal=Current Biology |language=en |volume=28 |issue=13 |pages=R727–R732 |doi=10.1016/j.cub.2018.05.021|pmid=29990451 |bibcode=2018CBio...28.R727L }}</ref> Most of those environments are not categorized as extreme and thus methanogens that inhabit them. However, many well studied methanogens are thermophiles such as ''[[Methanopyrus kandleri|Methanopyrus kandlerii]]'', ''[[Methanothermobacter marburgensis|Methanthermobacter marburgensis]]'', ''[[Methanocaldococcus jannaschii]]''. On the other hand, gut methanogens such as ''Methanobrevibacter smithii'' common in humans or ''Methanobrevibacter ruminantium'' omnipresent in ruminants are [[Mesophile|mesophiles]].
=== Methanogens in extreme environments ===
In deep [[basalt]]ic rocks near the [[mid-ocean ridge]]s, methanogens can obtain their [[hydrogen]] from the [[serpentinization]] reaction of [[olivine]] as observed in the [[Lost City (hydrothermal field)|hydrothermal field of Lost City]]. The thermal breakdown of water and water [[radiolysis]] are other possible sources of hydrogen. Methanogens are key agents of remineralization of [[organic carbon]] in [[continental margin]] sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of [[methane clathrate]]s<ref name="Kvenvolden 1995">{{cite journal| last=Kvenvolden| first= K.| date=1995| title= A review of the geochemistry of methane in natural gas hydrate| journal= Organic Geochemistry| volume=23| issue=11–12| pages=997–1008| doi= 10.1016/0146-6380(96)00002-2| bibcode= 1995OrGeo..23..997K}}</ref> that account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.<ref name="Milkov 2004">{{cite journal|last=Milkov| first=Alexei V| date=2004| title= Global estimates of hydrate-bound gas in marine sediments: how much is really out there?| journal= Earth-Science Reviews| volume=66| issue=3–4| pages=183–197| doi=10.1016/j.earscirev.2003.11.002| bibcode=2004ESRv...66..183M}}</ref>
Methanogens have been found in several extreme environments on Earth – buried under kilometres of ice in [[Greenland]] and living in hot, dry desert soil. They are known to be the most common archaea in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from about three kilometres under Greenland by researchers from the [[University of California, Berkeley]]. They also found a constant metabolism able to repair macromolecular damage, at temperatures of 145 to –40 °C.<ref name=":3">{{Cite journal|doi=10.1073/pnas.0507601102|title=Microbial origin of excess methane in glacial ice and implications for life on Mars|journal=Proceedings of the National Academy of Sciences|volume=102|issue=51|pages=18292–6|year=2005|last1=Tung|first1=H. C.|last2=Bramall|first2=N. E.|last3=Price|first3=P. B.|pmid=16339015|pmc=1308353|bibcode=2005PNAS..10218292T|doi-access=free}}</ref>
Another study<ref name=":4">Icarus (vol. 178, p. 277)cs:Methanogen</ref> has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in [[Utah]], [[Idaho]] and [[California]] in the [[United States]], and in [[Canada]] and [[Chile]]. Of these, five soil samples and three vapour samples from the vicinity of the [[Mars Desert Research Station]] in Utah were found to have signs of viable methanogens.<ref name=":5">{{Cite journal |last1=Michał |first1=Burdukiewicz |last2=Gagat |first2=Przemysław |last3=Jabłoński |first3=Sławomir |last4=Chilimoniuk |first4=Jarosław |last5=Gaworski |first5=Michał |last6=Mackiewicz |first6=Paweł |last7=Marcin |first7=Łukaszewicz |date=June 2018 |title=PhyMet 2 : a database and toolkit for phylogenetic and metabolic analyses of methanogens |journal=Environmental Microbiology Reports |language=en |volume=10 |issue=3 |pages=378–382 |doi=10.1111/1758-2229.12648 |issn=1758-2229|doi-access=free |pmid=29624889 |bibcode=2018EnvMR..10..378M }}</ref>
Some scientists have proposed that the presence of methane in the [[Mars|Martian]] atmosphere may be indicative of native methanogens on that planet.<ref>{{cite web|url=http://www.space.com/scienceastronomy/051220_science_tuesday.html|title=Crater Critters: Where Mars Microbes Might Lurk|work=Space.com|date=20 December 2005 |access-date=16 December 2014}}</ref> In June 2019, NASA's [[Curiosity (rover)|Curiosity]] rover detected methane, commonly generated by underground microbes such as methanogens, which signals possibility of [[life on Mars]].<ref>{{cite news|url=https://www.nytimes.com/2019/06/22/science/nasa-mars-rover-life.html|title=NASA Rover on Mars Detects Puff of Gas That Hints at Possibility of Life|work=The New York Times|date=22 June 2019}}</ref>
Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate.<ref>{{cite journal | doi=10.1038/440878a | author=Thauer, R. K. |author2=Shima, S. |name-list-style=amp | title=Biogeochemistry: Methane and microbes | journal = Nature | date = 2006 | volume = 440 | issue = 7086| pages=878–879 | pmid=16612369 |bibcode = 2006Natur.440..878T | s2cid=4373591 }}</ref> Most methanogens are [[autotrophic]] producers, but those that [[oxidize]] CH<sub>3</sub>COO<sup>−</sup> are classed as [[chemotroph]] instead.
=== Methanogens in the digestive tract of animals ===
The digestive tract of animals is characterized by a nutrient-rich and predominantly anaerobic environment, making it an ideal habitat for many microbes, including methanogens. Despite this, methanogens and archaea, in general, were largely overlooked as part of the gut microbiota until recently. However, they play a crucial role in maintaining gut balance by utilizing end products of bacterial fermentation, such as H<sub>2</sub>, acetate, methanol, and methylamines.
Recent extensive surveys of archaea presence in the animal gut, based on 16S rRNA analysis, have provided a comprehensive view of archaea diversity and abundance.<ref>{{Cite journal |last1=Youngblut |first1=Nicholas D. |last2=Reischer |first2=Georg H. |last3=Dauser |first3=Silke |last4=Maisch |first4=Sophie |last5=Walzer |first5=Chris |last6=Stalder |first6=Gabrielle |last7=Farnleitner |first7=Andreas H. |last8=Ley |first8=Ruth E. |date=2021-10-26 |title=Vertebrate host phylogeny influences gut archaeal diversity |journal=Nature Microbiology |language=en |volume=6 |issue=11 |pages=1443–1454 |doi=10.1038/s41564-021-00980-2 |issn=2058-5276 |pmc=8556154 |pmid=34702978}}</ref><ref>{{Cite journal |last1=Thomas |first1=Courtney M. |last2=Desmond-Le Quéméner |first2=Elie |last3=Gribaldo |first3=Simonetta |last4=Borrel |first4=Guillaume |date=2022-06-10 |title=Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom |journal=Nature Communications |language=en |volume=13 |issue=1 |page=3358 |doi=10.1038/s41467-022-31038-4 |issn=2041-1723 |pmc=9187648 |pmid=35688919|bibcode=2022NatCo..13.3358T }}</ref><ref>{{Cite journal |last1=Protasov |first1=Evgenii |last2=Nonoh |first2=James O. |last3=Kästle Silva |first3=Joana M. |last4=Mies |first4=Undine S. |last5=Hervé |first5=Vincent |last6=Dietrich |first6=Carsten |last7=Lang |first7=Kristina |last8=Mikulski |first8=Lena |last9=Platt |first9=Katja |last10=Poehlein |first10=Anja |last11=Köhler-Ramm |first11=Tim |last12=Miambi |first12=Edouard |last13=Boga |first13=Hamadi I. |last14=Feldewert |first14=Christopher |last15=Ngugi |first15=David K. |date=2023-11-15 |title=Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods |journal=Frontiers in Microbiology |volume=14 |doi=10.3389/fmicb.2023.1281628 |doi-access=free |issn=1664-302X |pmc=10684969 |pmid=38033561}}</ref> These studies revealed that only a few archaeal lineages are present, with the majority being methanogens, while non-methanogenic archaea are rare and not abundant. Taxonomic classification of archaeal diversity identified that representatives of only three phyla are present in the digestive tracts of animals: ''Methanobacteriota'' (order ''Methanobacteriales''), ''Thermoplasmatota'' (order ''Methanomassiliicoccales''), and ''Halobacteriota'' (orders ''Methanomicrobiales'' and ''Methanosarcinales''). However, not all families and genera within these orders were detected in animal guts, but only a few genera, suggesting their specific adaptations to the gut environment.
==Comparative genomics and molecular signatures==
Comparative proteomic analysis has led to the identification of 31 signature proteins which are specific for methanogens (also known as ''Methanoarchaeota''). Most of these proteins are related to methanogenesis, and they could serve as potential molecular markers for methanogens. Additionally, 10 proteins found in all methanogens which are shared by ''[[Archaeoglobus]]'', suggest that these two groups are related. In phylogenetic trees, methanogens are not monophyletic and they are generally split into three clades. Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.<ref>{{Cite journal|last1=Gao|first1=Beile|last2=Gupta|first2=Radhey S|date=2007|title=Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis|journal=BMC Genomics|volume=8|issue=1|pages=86|doi=10.1186/1471-2164-8-86|pmc=1852104|pmid=17394648 |doi-access=free }}</ref> Additionally, more recent novel proteins associated with sulfide trafficking have been linked to methanogen archaea.<ref>{{Cite journal|last1=Rauch|first1=Benjamin Julius|last2=Gustafson|first2=Andrew|last3=Perona|first3=John J.|date=December 2014|title=Novel proteins for homocysteine biosynthesis in anaerobic microorganisms|journal=Molecular Microbiology|language=en|volume=94|issue=6|pages=1330–1342|doi=10.1111/mmi.12832|pmid=25315403|issn=0950-382X|doi-access=free}}</ref> More proteomic analysis is needed to further differentiate specific genera within the methanogen class and reveal novel pathways for methanogenic metabolism.
Modern DNA or RNA sequencing approaches has elucidated several genomic markers specific to several groups of methanogens. One such finding isolated nine methanogens from genus Methanoculleus and found that there were at least 2 trehalose synthases genes that were found in all nine genomes.<ref>{{Cite journal|last1=Chen|first1=Sheng-Chung|last2=Weng|first2=Chieh-Yin|last3=Lai|first3=Mei-Chin|last4=Tamaki|first4=Hideyuki|last5=Narihiro|first5=Takashi|date=October 2019|title=Comparative genomic analyses reveal trehalose synthase genes as the signature in genus Methanoculleus|journal=Marine Genomics|language=en|volume=47|pages=100673|doi=10.1016/j.margen.2019.03.008|pmid=30935830|bibcode=2019MarGn..4700673C |s2cid=91188321 |doi-access=
Genomic signatures not only allow one to mark unique methanogens and genes relevant to environmental conditions; it has also led to a better understanding of the evolution of these archaea. Some methanogens must actively mitigate against oxic environments. Functional genes involved with the production of antioxidants have been found in methanogens, and some specific groups tend to have an enrichment of this genomic feature. Methanogens containing a genome with enriched antioxidant properties may provide evidence that this genomic addition may have occurred during the Great Oxygenation Event.<ref>{{Cite journal|last1=Lyu|first1=Zhe|last2=Lu|first2=Yahai|date=February 2018|title=Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments|journal=The ISME Journal|language=en|volume=12|issue=2|pages=411–423|doi=10.1038/ismej.2017.173|issn=1751-7362|pmc=5776455|pmid=29135970|bibcode=2018ISMEJ..12..411L }}</ref> In another study, three strains from the lineage Thermoplasmatales isolated from animal gastro-intestinal tracts revealed evolutionary differences. The eukaryotic-like histone gene which is present in most methanogen genomes was not present, eluding to evidence that an ancestral branch was lost within Thermoplasmatales and related lineages.<ref>{{Cite journal|last1=Borrel|first1=Guillaume|last2=Parisot|first2=Nicolas|last3=Harris|first3=Hugh MB|last4=Peyretaillade|first4=Eric|last5=Gaci|first5=Nadia|last6=Tottey|first6=William|last7=Bardot|first7=Olivier|last8=Raymann|first8=Kasie|last9=Gribaldo|first9=Simonetta|last10=Peyret|first10=Pierre|last11=O’Toole|first11=Paul W|date=2014|title=Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine|journal=BMC Genomics|language=en|volume=15|issue=1|pages=679|doi=10.1186/1471-2164-15-679|issn=1471-2164|pmc=4153887|pmid=25124552 |doi-access=free }}</ref> Furthermore, the group Methanomassiliicoccus has a genome which appears to have lost many common genes coding for the first several steps of methanogenesis. These genes appear to have been replaced by genes coding for a novel methylated methogenic pathway. This pathway has been reported in several types of environments, pointing to non-environment specific evolution, and may point to an ancestral deviation.<ref>{{Cite journal|last1=Borrel|first1=Guillaume|last2=O’Toole|first2=Paul W.|last3=Harris|first3=Hugh M.B.|last4=Peyret|first4=Pierre|last5=Brugère|first5=Jean-François|last6=Gribaldo|first6=Simonetta|date=October 2013|title=Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis|journal=Genome Biology and Evolution|language=en|volume=5|issue=10|pages=1769–1780|doi=10.1093/gbe/evt128|issn=1759-6653|pmc=3814188|pmid=23985970}}</ref>
== Metabolism ==
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:<chem>CO2 + 4 H2 -> CH4 + 2 H2O</chem> (∆G˚’ = -134 kJ/mol CH<sub>4</sub>)
Well-studied organisms that produce methane via H<sub>2</sub>/CO<sub>2</sub> methanogenesis include ''Methanosarcina barkeri'', ''Methanobacterium thermoautotrophicum'', and ''Methanobacterium wolfei''.<ref>{{Cite journal|last1=Karrasch|first1=M.|last2=Börner|first2=G.|last3=Enssle|first3=M.|last4=Thauer|first4=R. K.|date=1990-12-12|title=The molybdoenzyme formylmethanofuran dehydrogenase from Methanosarcina barkeri contains a pterin cofactor|journal=European Journal of Biochemistry|volume=194|issue=2|pages=367–372|issn=0014-2956|pmid=2125267|doi=10.1111/j.1432-1033.1990.tb15627.x}}</ref><ref>{{Cite journal|last1=Börner|first1=G.|last2=Karrasch|first2=M.|last3=Thauer|first3=R. K.|date=1991-09-23|title=Molybdopterin adenine dinucleotide and molybdopterin hypoxanthine dinucleotide in formylmethanofuran dehydrogenase from Methanobacterium thermoautotrophicum (Marburg)|journal=FEBS Letters|volume=290|issue=1–2|pages=31–34|issn=0014-5793|pmid=1915887|doi=10.1016/0014-5793(91)81218-w|s2cid=24174561|doi-access=free|bibcode=1991FEBSL.290...31B }}</ref><ref>{{Cite journal|last1=Schmitz|first1=Ruth A.|last2=Albracht|first2=Simon P. J.|last3=Thauer|first3=Rudolf K.|date=1992-11-01|title=A molybdenum and a tungsten isoenzyme of formylmethanofuran dehydrogenase in the thermophilic archaeon Methanobacterium wolfei|journal=European Journal of Biochemistry|language=en|volume=209|issue=3|pages=1013–1018|doi=10.1111/j.1432-1033.1992.tb17376.x|pmid=1330558|issn=1432-1033|doi-access=free}}</ref> These organisms are typically found in anaerobic environments.<ref name=":6" />
In the earliest stage of H<sub>2</sub>/CO<sub>2</sub> methanogenesis, CO<sub>2</sub> binds to [[methanofuran]] (MF) and is reduced to formyl-MF. This [[Endergonic reaction|endergonic]] reductive process (∆G˚’= +16 kJ/mol) is dependent on the availability of H<sub>2</sub> and is catalyzed by the enzyme formyl-MF dehydrogenase.<ref name=":6" />
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:<chem>HCO-MF + H4MPT -> HCO-H4MPT + MF</chem>
Formyl-H4MPT is subsequently reduced to methenyl-H4MPT. Methenyl-H4MPT then undergoes a one-step hydrolysis followed by a two-step reduction to methyl-H4MPT. The two-step reversible reduction is assisted by [[Coenzyme F420|coenzyme F<sub>420</sub>]] whose hydride acceptor spontaneously oxidizes.<ref name=":6" /> Once oxidized, F<sub>420</sub>’s electron supply is replenished by accepting electrons from H<sub>2</sub>. This step is catalyzed by methylene H4MPT dehydrogenase.<ref>{{Cite journal|last=Zirngibl|first=C|date=February 1990|title=N5,N10-Methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum has hydrogenase activity|journal=Laboratorium Fir Mikrobiologie|volume=261 | issue = 1 |pages=112–116|doi=10.1016/0014-5793(90)80649-4|doi-access=free|bibcode=1990FEBSL.261..112Z}}</ref>
:<chem>HCO-H4MPT + H+ -> CH-H4MPT+ + H2O</chem> (Formyl-H4MPT reduction)
Line 82 ⟶ 61:
:<chem>CH2=H4MPT + H2 -> CH3-H4MPT + H+</chem>(H4MPT reduction)
Next, the methyl group of methyl-M4MPT is transferred to coenzyme M via a methyltransferase-catalyzed reaction.<ref>{{Cite journal|last1=te Brömmelstroet|first1=B. W.|last2=Geerts|first2=W. J.|last3=Keltjens|first3=J. T.|last4=van der Drift|first4=C.|last5=Vogels|first5=G. D.|date=1991-09-20|title=Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri|journal=Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology|volume=1079|issue=3|pages=293–302|issn=0006-3002|pmid=1911853|doi=10.1016/0167-4838(91)90072-8}}</ref><ref>{{Cite journal|last1=Kengen|first1=Servé W. M.|last2=Mosterd|first2=Judith J.|last3=Nelissen|first3=Rob L. H.|last4=Keltjens|first4=Jan T.|last5=Drift|first5=Chris van der|last6=Vogels|first6=Godfried D.|date=1988-08-01|title=Reductive activation of the methyl-tetrahydromethanopterin: coenzyme M methyltransferase from Methanobacterium thermoautotrophicum strain ΔH|journal=Archives of Microbiology|language=en|volume=150|issue=4|pages=405–412|doi=10.1007/BF00408315|bibcode=1988ArMic.150..405K |s2cid=36366503|issn=0302-8933}}</ref>
:<chem>CH3-H4MPT + HS-CoM -> CH3-S-CoM + H4MPT</chem>
Line 91 ⟶ 70:
:<chem>CoM-S-S-HTP + H2 -> HS-CoM + HS-HTP</chem> (Regeneration of coenzyme M)
:
== Biotechnological application ==
=== Wastewater treatment ===
Methanogens are widely used in anaerobic digestors to treat wastewater as well as aqueous organic pollutants. Industries have selected methanogens for their ability to perform [[biomethanation]] during wastewater decomposition thereby rendering the process sustainable and cost-effective.<ref>Appels, Lise; et al. (2008). "Principles and potential of the anaerobic digestion of waste-activated sludge" Progress in Energy and Combustion Science. 34 (6): 755 -781. doi: 10.1016/j.pecs.2008.06.002</ref>
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The organic components of wastewater vary vastly. Chemical structures of the organic matter select for specific methanogens to perform anaerobic digestion. An example is the members of ''[[Methanosaeta]]'' genus dominate the digestion of palm oil mill effluent (POME) and brewery waste.<ref name="doi_10.1016/j.procbio.2010.05.017"/> Modernizing wastewater treatment systems to incorporate higher diversity of microorganisms to decrease organic content in treatment is under active research in the field of microbiological and chemical engineering.<ref>Marihiro, Takashi., Sekiguchi, Yuji. (2007). "Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update" Current Opinion in Biotechnology. 18 (3): 273-278. doi: 10.1016/j.copbio.2007.04.003</ref> Current new generations of Staged Multi-Phase Anaerobic reactors and Upflow Sludge Bed reactor systems are designed to have innovated features to counter high loading wastewater input, extreme temperature conditions, and possible inhibitory compounds.<ref>{{cite journal|doi=10.1016/S0273-1223(97)00222-9|title=Advanced anaerobic wastewater treatment in the near future|journal=Water Science and Technology|volume=35|issue=10|year=1997}}</ref>
==
Initially, methanogens were considered to be bacteria, as it was not possible to distinguish archaea and bacteria before the introduction of molecular techniques such as DNA sequencing and PCR. Since the introduction of the domain Archaea by Carl Woese in 1977,<ref>{{Cite journal |last1=Woese |first1=Carl R. |last2=Fox |first2=George E. |date=November 1977 |title=Phylogenetic structure of the prokaryotic domain: The primary kingdoms |journal=Proceedings of the National Academy of Sciences |language=en |volume=74 |issue=11 |pages=5088–5090 |doi=10.1073/pnas.74.11.5088 |doi-access=free |issn=0027-8424 |pmc=432104 |pmid=270744|bibcode=1977PNAS...74.5088W }}</ref> methanogens were for a prolonged period considered a monophyletic group, later named Euryarchaeota (super)phylum. However, intensive studies of various environments have proved that there are more and more non-methanogenic lineages among methanogenic ones.
The development of genome sequencing directly from environmental samples (metagenomics) allowed the discovery of the first methanogens outside the Euryarchaeota superphylum. The first such putative methanogenic lineage was Bathyarchaeia,<ref>{{Cite journal |last1=Evans |first1=Paul N. |last2=Parks |first2=Donovan H. |last3=Chadwick |first3=Grayson L. |last4=Robbins |first4=Steven J. |last5=Orphan |first5=Victoria J. |last6=Golding |first6=Suzanne D. |last7=Tyson |first7=Gene W. |date=2015-10-23 |title=Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics |url=https://www.science.org/doi/10.1126/science.aac7745 |journal=Science |language=en |volume=350 |issue=6259 |pages=434–438 |doi=10.1126/science.aac7745 |pmid=26494757 |bibcode=2015Sci...350..434E |issn=0036-8075}}</ref> a class within the Thermoproteota phylum. Later, it was shown that this lineage is not methanogenic but alkane-oxidizing utilizing highly divergent enzyme Acr similar to the hallmark gene of methanogenesis, methyl-CoM reductase (McrABG).<ref>{{Cite journal |last1=Qi |first1=Yan-Ling |last2=Evans |first2=Paul N. |last3=Li |first3=Yu-Xian |last4=Rao |first4=Yang-Zhi |last5=Qu |first5=Yan-Ni |last6=Tan |first6=Sha |last7=Jiao |first7=Jian-Yu |last8=Chen |first8=Ya-Ting |last9=Hedlund |first9=Brian P. |last10=Shu |first10=Wen-Sheng |last11=Hua |first11=Zheng-Shuang |last12=Li |first12=Wen-Jun |date=2021-08-31 |title=Comparative Genomics Reveals Thermal Adaptation and a High Metabolic Diversity in ''Candidatus'' Bathyarchaeia" |url=http://dx.doi.org/10.1128/msystems.00252-21 |journal=mSystems |volume=6 |issue=4 |pages=e0025221 |doi=10.1128/msystems.00252-21 |pmid=34282939 |pmc=8407382 |issn=2379-5077}}</ref> The first isolate of Bathyarchaeum tardum from sediment of coastal lake in Russia showed that it metabolizes aromatic compounds and proteins<ref>{{Cite journal |last1=Khomyakova |first1=Maria A. |last2=Merkel |first2=Alexander Y. |last3=Mamiy |first3=Dana D. |last4=Klyukina |first4=Alexandra A. |last5=Slobodkin |first5=Alexander I. |date=2023-08-22 |title=Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia |journal=Frontiers in Microbiology |volume=14 |doi=10.3389/fmicb.2023.1214631 |doi-access=free |issn=1664-302X |pmc=10477458 |pmid=37675420}}</ref> as it was previously predicted based on metagenomic studies.<ref>{{Cite journal |last1=Zhou |first1=Zhichao |last2=Pan |first2=Jie |last3=Wang |first3=Fengping |last4=Gu |first4=Ji-Dong |last5=Li |first5=Meng |date=2018-09-01 |title=Bathyarchaeota: globally distributed metabolic generalists in anoxic environments |url=https://academic.oup.com/femsre/article/42/5/639/5000165 |journal=FEMS Microbiology Reviews |language=en |volume=42 |issue=5 |pages=639–655 |doi=10.1093/femsre/fuy023 |pmid=29790926 |issn=1574-6976}}</ref><ref>{{Cite journal |last1=Yu |first1=Tiantian |last2=Wu |first2=Weichao |last3=Liang |first3=Wenyue |last4=Lever |first4=Mark Alexander |last5=Hinrichs |first5=Kai-Uwe |last6=Wang |first6=Fengping |date=2018-06-05 |title=Growth of sedimentary Bathyarchaeota on lignin as an energy source |journal=Proceedings of the National Academy of Sciences |language=en |volume=115 |issue=23 |pages=6022–6027 |doi=10.1073/pnas.1718854115 |doi-access=free |issn=0027-8424 |pmc=6003339 |pmid=29773709|bibcode=2018PNAS..115.6022Y }}</ref><ref>{{Cite journal |last1=Yu |first1=Tiantian |last2=Hu |first2=Haining |last3=Zeng |first3=Xianhong |last4=Wang |first4=Yinzhao |last5=Pan |first5=Donald |last6=Deng |first6=Longhui |last7=Liang |first7=Lewen |last8=Hou |first8=Jialin |last9=Wang |first9=Fengping |date=September 2023 |title=Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics |journal=mLife |language=en |volume=2 |issue=3 |pages=272–282 |doi=10.1002/mlf2.12082 |issn=2097-1699 |pmc=10989822 |pmid=38817817}}</ref> However, more new putative methanogens outside of Euryarchaeota were discovered based on the presence McrABG.
For instance, methanogens were found in the phyla Thermoproteota (orders Methanomethyliales, Korarchaeales, Methanohydrogenales, Nezhaarchaeales) and Methanobacteriota_B (order Methanofastidiosales). Additionally, some new lineages of methanogens were isolated in pure culture, which allowed the discovery of a new type of methanogenesis: H<sub>2</sub>-dependent methyl-reducing methanogenesis, which is independent of the Wood-Ljungdahl pathway. For example, in 2012, the order ''Methanoplasmatales'' from the phylum ''Thermoplasmatota'' was described as a seventh order of methanogens.<ref>{{Cite journal |last1=Paul |first1=Kristina |last2=Nonoh |first2=James O. |last3=Mikulski |first3=Lena |last4=Brune |first4=Andreas |date=December 2012 |title="Methanoplasmatales," Thermoplasmatales-Related Archaea in Termite Guts and Other Environments, Are the Seventh Order of Methanogens |url=http://dx.doi.org/10.1128/aem.02193-12 |journal=Applied and Environmental Microbiology |volume=78 |issue=23 |pages=8245–8253 |doi=10.1128/aem.02193-12 |pmid=23001661 |pmc=3497382 |bibcode=2012ApEnM..78.8245P |issn=0099-2240}}</ref> Later, the order was renamed ''Methanomassiliicoccales'' based on the isolated from human gut ''Methanomassiliicoccus luminyensis''.<ref>{{Cite journal |last1=Dridi |first1=Bédis |last2=Fardeau |first2=Marie-Laure |last3=Ollivier |first3=Bernard |last4=Raoult |first4=Didier |last5=Drancourt |first5=Michel |date=2012-08-01 |title=Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.033712-0 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=62 |issue=Pt_8 |pages=1902–1907 |doi=10.1099/ijs.0.033712-0 |pmid=22859731 |issn=1466-5026}}</ref><ref>{{Cite journal |last1=Iino |first1=Takao |last2=Tamaki |first2=Hideyuki |last3=Tamazawa |first3=Satoshi |last4=Ueno |first4=Yoshiyuki |last5=Ohkuma |first5=Moriya |last6=Suzuki |first6=Ken-ichiro |last7=Igarashi |first7=Yasuo |last8=Haruta |first8=Shin |date=2013 |title=Candidatus Methanogranum caenicola: a Novel Methanogen from the Anaerobic Digested Sludge, and Proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a Methanogenic Lineage of the Class Thermoplasmata |url=https://www.jstage.jst.go.jp/article/jsme2/28/2/28_ME12189/_article |journal=Microbes and Environments |language=en |volume=28 |issue=2 |pages=244–250 |doi=10.1264/jsme2.ME12189 |issn=1342-6311 |pmc=4070666 |pmid=23524372}}</ref>
Another new lineage in the ''Halobacteriota'' phylum, order ''Methanonatronarchaeales'', was discovered in alkaline saline lakes in Siberia in 2017.<ref>{{Cite journal |last1=Sorokin |first1=Dimitry Y. |last2=Merkel |first2=Alexander Y. |last3=Abbas |first3=Ben |last4=Makarova |first4=Kira S. |last5=Rijpstra |first5=W. Irene C. |last6=Koenen |first6=M. |last7=Sinninghe Damsté |first7=Jaap S. |last8=Galinski |first8=Erwin A. |last9=Koonin |first9=Eugene V. |last10=van Loosdrecht |first10=Mark C. M. |date=2018-07-01 |title=Methanonatronarchaeum thermophilum gen. nov., sp. nov. and 'Candidatus Methanohalarchaeum thermophilum', extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=68 |issue=7 |pages=2199–2208 |doi=10.1099/ijsem.0.002810 |issn=1466-5026 |pmc=6978985 |pmid=29781801}}</ref><ref>{{Cite journal |last1=Sorokin |first1=Dimitry Y. |last2=Makarova |first2=Kira S. |last3=Abbas |first3=Ben |last4=Ferrer |first4=Manuel |last5=Golyshin |first5=Peter N. |last6=Galinski |first6=Erwin A. |last7=Ciordia |first7=Sergio |last8=Mena |first8=María Carmen |last9=Merkel |first9=Alexander Y. |last10=Wolf |first10=Yuri I. |last11=van Loosdrecht |first11=Mark C. M. |last12=Koonin |first12=Eugene V. |date=2017-05-30 |title=Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis |journal=Nature Microbiology |language=en |volume=2 |issue=8 |page=17081 |doi=10.1038/nmicrobiol.2017.81 |issn=2058-5276 |pmc=5494993 |pmid=28555626}}</ref> It also employs H<sub>2</sub>-dependent methyl-reducing methanogenesis but intriguingly harbors almost the full Wood-Ljungdahl pathway. However, it is disconnected from McrABG as no MtrA-H complex was detected.<ref>{{Cite journal |last1=Sorokin |first1=Dimitry Y. |last2=Merkel |first2=Alexander Y. |last3=Abbas |first3=Ben |date=November 2022 |title=Ecology of Methanonatronarchaeia |journal=Environmental Microbiology |language=en |volume=24 |issue=11 |pages=5217–5229 |doi=10.1111/1462-2920.16108 |issn=1462-2912 |pmc=9796771 |pmid=35726892|bibcode=2022EnvMi..24.5217S }}</ref><ref>{{Cite journal |last1=Steiniger |first1=Fabian |last2=Sorokin |first2=Dimitry Y. |last3=Deppenmeier |first3=Uwe |date=January 2022 |title=Process of energy conservation in the extremely haloalkaliphilic methyl-reducing methanogen Methanonatronarchaeum thermophilum |url=https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.16165 |journal=The FEBS Journal |language=en |volume=289 |issue=2 |pages=549–563 |doi=10.1111/febs.16165 |pmid=34435454 |issn=1742-464X}}</ref>
The [[Taxonomy (biology)|taxonomy]] of methanogens reflects the evolution of these [[archaea]], with some studies suggesting that the Last Archaeal Common Ancestor was methanogenic.<ref>{{Cite journal |last1=Mei |first1=Ran |last2=Kaneko |first2=Masanori |last3=Imachi |first3=Hiroyuki |last4=Nobu |first4=Masaru K |date=2023-02-03 |editor-last=Ma |editor-first=Li-Jun |title=The origin and evolution of methanogenesis and Archaea are intertwined |url=https://academic.oup.com/pnasnexus/article/doi/10.1093/pnasnexus/pgad023/7010768 |journal=PNAS Nexus |language=en |volume=2 |issue=2 |pages=pgad023 |doi=10.1093/pnasnexus/pgad023 |issn=2752-6542 |pmc=9982363 |pmid=36874274}}</ref> If correct, this suggests that many archaeal lineages lost the ability to produce methane and switched to other types of metabolism. Currently, most of the isolated methanogens belong to one of three archaeal phyla ([[List of Archaea genera|classification]] GTDB release 220): ''Halobacteriota'', ''Methanobacteriota'', and ''Thermoplasmatota''. Under the International Code of Nomenclature for Prokaryotes,<ref>{{Cite journal |last1=Oren |first1=Aharon |last2=Arahal |first2=David R. |last3=Göker |first3=Markus |last4=Moore |first4=Edward R. B. |last5=Rossello-Mora |first5=Ramon |last6=Sutcliffe |first6=Iain C. |date=2023-05-01 |title=International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision) |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005585 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=73 |issue=5a |doi=10.1099/ijsem.0.005585 |pmid=37219928 |issn=1466-5026|hdl=10261/338243 |hdl-access=free }}</ref> all three phyla belong to the same kingdom, ''Methanobacteriati''.<ref>{{Cite web |title=Phylum: Methanobacteriota |url=https://lpsn.dsmz.de/phylum/methanobacteriota |access-date=2024-07-16 |website=lpsn.dsmz.de |language=en}}</ref><ref>{{Cite journal |last1=Göker |first1=Markus |last2=Oren |first2=Aharon |date=2024-01-22 |title=Valid publication of names of two domains and seven kingdoms of prokaryotes |url=https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006242 |journal=International Journal of Systematic and Evolutionary Microbiology |language=en |volume=74 |issue=1 |doi=10.1099/ijsem.0.006242 |pmid=38252124 |issn=1466-5026}}</ref> In total, more than 150 methanogen species are known in culture, with some represented by more than one [[Strain (biology)|strain]].<ref>{{Cite web |title=Leibniz Institute DSMZ: Welcome to the Leibniz Institute DSMZ |url=https://www.dsmz.de/ |access-date=2024-07-16 |website=www.dsmz.de |language=en-US}}</ref>
=== Phylum ''Halobacteriota'' ===
==== '''Class ''Methanocellia''''' ====
===== Order ''Methanocellales'' =====
====== Family ''Methanocellaceae'' ======
Genus ''Methanocella'' Sakai et al. 2008
''Methanocella'' ''paludicola'' Sakai ''et al.'' 2008 (type species)
''Methanocella'' ''arvoryzae'' Sakai ''et al.'' 2010
''Methanocella'' ''conradii'' Lü and Lu 2012
==== '''Class ''Methanomicrobia''''' ====
===== Order ''[[Methanomicrobiales]]'' =====
====== Family ''[[Methanocalculaceae]]'' Zhilina ''et al.'' 2014 ======
====== Family ''[[Methanocorpusculaceae]]'' Zellner ''et al.'' 1989 ======
''[[Methanocorpusculum]]'' Zellner ''et al.'' 1988
''Methanocorpusculum'' ''parvum'' Zellner ''et al.'' 1988 (type species)
''Methanocorpusculum'' ''bavaricum'' Zellner ''et al.'' 1989
''[[Methanocorpusculum labreanum]]''
''Methanocorpusculum'' ''sinense'' Zellner ''et al.'' 1989
====== Family ''[[Methanomicrobiaceae]]'' Balch and Wolfe 1981 ======
Genus ''[[Methanomicrobium]]'' Balch and Wolfe 1981
[[Methanomicrobium mobile|''Methanomicrobium'' ''mobile'']] (Paynter and Hungate 1968) Balch and Wolfe 1981 (type species)
''Methanomicrobium'' ''antiquum'' Mochimaru ''et al.'' 2016
Genus ''[[Methanoculleus]]'' Maestrojuán ''et al.'' 1990
[[Methanoculleus bourgensis|''Methanoculleus'' ''bourgensis'']] corrig. (Ollivier ''et al.'' 1986) Maestrojuán ''et al.'' 1990 (type species)
''Methanoculleus'' ''chikugoensis'' Dianou ''et al.'' 2001
''Methanoculleus'' ''horonobensis'' Shimizu ''et al.'' 2013
''Methanoculleus'' ''hydrogenitrophicus'' Tian ''et al.'' 2010
''[[Methanoculleus marisnigri]]''
''Methanoculleus'' ''palmolei'' Zellner ''et al.'' 1998
''Methanoculleus'' ''receptaculi'' Cheng ''et al.'' 2008
''Methanoculleus'' ''sediminis'' Chen ''et al.'' 2015
''Methanoculleus'' ''submarinus'' Mikucki ''et al.'' 2003
''Methanoculleus'' ''taiwanensis'' Weng ''et al.'' 2015
''Methanoculleus'' ''thermophilus'' corrig. (Rivard and Smith 1982) Maestrojuán ''et al.'' 1990
Genus ''[[Methanogenium]]'' Romesser ''et al.'' 1981
[[Methanogenium cariaci|''Methanogenium'' ''cariaci'']] Romesser ''et al.'' 1981 (type species)
''[[Methanogenium frigidum]]''
''Methanogenium'' ''marinum'' Chong ''et al.'' 2003
''[[Methanogenium organophilum]]''
Genus ''[[Methanofollis]]'' Zellner ''et al.'' 1999
''Methanofollis'' ''tationis'' (Zabel ''et al.'' 1986) Zellner ''et al.'' 1999 (type strains)
''Methanofollis'' ''aquaemaris'' Lai and Chen 2001
''Methanofollis'' ''ethanolicus'' Imachi ''et al.'' 2009
''Methanofollis'' ''fontis'' Chen ''et al.'' 2020
''Methanofollis'' ''formosanus'' Wu ''et al.'' 2005
[[Methanofollis liminatans|''Methanofollis'' ''liminatans'']] (Zellner ''et al.'' 1990) Zellner ''et al.'' 1999
====== Family ''[[Methanoregulaceae]]'' Sakai ''et al.'' 2012 ======
Genus ''[[Methanoregula]]'' Bräuer ''et al.'' 2011
[[Methanoregula boonei|''Methanoregula'' ''boonei'']] Bräuer ''et al.'' 2011 (type species)
''Methanoregula'' ''formicica'' Yashiro ''et al.'' 2011
====== Family ''[[Methanospirillaceae]]'' Boone ''et al.'' 2002 ======
''[[Methanospirillum]]'' Ferry ''et al.'' 1974
[[Methanospirillum hungatei|''Methanospirillum'' ''hungatei'']] corrig. Ferry ''et al.'' 1974 (type species)
''Methanospirillum'' ''lacunae'' Iino ''et al.'' 2010
''Methanospirillum'' ''psychrodurum'' Zhou ''et al.'' 2014
''Methanospirillum'' ''stamsii'' Parshina ''et al.'' 2014
==== '''Class ''[[Methanonatronarchaeia]]''''' ====
===== Order ''[[Methanonatronarchaeales]]'' =====
====== Family ''[[Methanonatronarchaeaceae]]'' Sorokin ''et al.'' 2018 ======
Genus ''[[Methanonatronarchaeum]]'' Sorokin ''et al.'' 2018
[[Methanonatronarchaeum thermophilum|''Methanonatronarchaeum'' ''thermophilum'']] Sorokin ''et al.'' 2018 (type species)
==== '''Class ''Methanosarcinia''''' ====
===== Order ''[[Methanosarcinales]]'' =====
====== Family ''[[Methanosarcinaceae]]'' ======
Genus ''[[Methanosarcina]]'' Kluyver and van Niel 1936
[[Methanosarcina barkeri|''Methanosarcina'' ''barkeri'']] Schnellen 1947 (type species)
''[[Methanosarcina acetivorans]]''
''Methanosarcina'' ''baltica'' von Klein ''et al.'' 2002
''Methanosarcina'' ''flavescens'' Kern ''et al.'' 2016
''Methanosarcina'' ''horonobensis'' Shimizu ''et al.'' 2011
''Methanosarcina'' ''lacustris'' Simankova ''et al.'' 2002
''[[Methanosarcina mazei]]'' (Barker 1936) Mah and Kuhn 1984
''Methanosarcina'' ''semesiae'' Lyimo ''et al.'' 2000
''Methanosarcina'' ''siciliae'' (Stetter and König 1989) Ni ''et al.'' 1994
''Methanosarcina'' ''soligelidi'' Wagner ''et al.'' 2013
''Methanosarcina'' ''spelaei'' Ganzert ''et al.'' 2014
''Methanosarcina'' ''subterranea'' Shimizu ''et al.'' 2015
''Methanosarcina'' ''thermophila'' Zinder ''et al.'' 1985
''Methanosarcina'' ''vacuolata'' Zhilina and Zavarzin 1987
Genus ''[[Methanimicrococcus]]'' corrig. Sprenger ''et al.'' 2000
[[Methanimicrococcus blatticola|''Methanimicrococcus'' ''blatticola'']] corrig. Sprenger ''et al.'' 2000
Genus ''[[Methanococcoides]]'' Sowers and Ferry 1985
[[Methanococcoides methylutens|''Methanococcoides'' ''methylutens'']] Sowers and Ferry 1985 (type species)
''Methanococcoides'' ''alaskense'' Singh ''et al.'' 2005
[[Methanococcoides burtonii|''Methanococcoides'' ''burtonii'']] Franzmann ''et al.'' 1993
''Methanococcoides'' ''orientis'' Liang ''et al.'' 2022
''Methanococcoides'' ''vulcani'' L'Haridon ''et al.'' 2014
Genus ''[[Methanohalobium]]'' Zhilina and Zavarzin 1988
[[Methanohalobium evestigatum|''Methanohalobium'' ''evestigatum'']] corrig. Zhilina and Zavarzin 1988 (type species)
Genus ''[[Methanohalophilus]]'' Paterek and Smith 1988
[[Methanohalophilus mahii|''Methanohalophilus'' ''mahii'']] Paterek and Smith 1988 (type species)
''Methanohalophilus'' ''halophilus'' (Zhilina 1984) Wilharm ''et al.'' 1991
''Methanohalophilus'' ''levihalophilus'' Katayama ''et al.'' 2014
''Methanohalophilus'' ''portucalensis'' Boone ''et al.'' 1993
''Methanohalophilus'' ''profundi'' L'Haridon ''et al.'' 2021
Genus ''[[Methanolobus]]'' König and Stetter 1983
[[Methanolobus tindarius|''Methanolobus'' ''tindarius'']] König and Stetter 1983 (type species)
[[Methanolobus bombayensis|''Methanolobus'' ''bombayensis'']] Kadam ''et al.'' 1994
''Methanolobus'' ''chelungpuianus'' Wu and Lai 2015
''Methanolobus'' ''halotolerans'' Shen ''et al.'' 2020
''Methanolobus'' ''mangrovi'' Zhou ''et al.'' 2023
''Methanolobus'' ''oregonensis'' (Liu ''et al.'' 1990) Boone 2002
''Methanolobus'' ''profundi'' Mochimaru ''et al.'' 2009
''Methanolobus'' ''psychrotolerans'' Chen ''et al.'' 2018
''Methanolobus'' ''sediminis'' Zhou ''et al.'' 2023
''Methanolobus'' ''taylorii'' Oremland and Boone 1994
''Methanolobus'' ''vulcani'' Stetter ''et al.'' 1989
''Methanolobus'' ''zinderi'' Doerfert ''et al.'' 2009
Genus ''[[Methanomethylovorans]]'' Lomans ''et al.'' 2004
[[Methanomethylovorans hollandica|''Methanomethylovorans'' ''hollandica'']] Lomans ''et al.'' 2004 (type species)
''Methanomethylovorans'' ''thermophila'' Jiang ''et al.'' 2005
''Methanomethylovorans'' ''uponensis'' Cha ''et al.'' 2014
Genus ''[[Methanosalsum]]'' Boone and Baker 2002
''Methanosalsum'' ''zhilinae'' (Mathrani ''et al.'' 1988) Boone and Baker 2002 (type species)
''Methanosalsum'' ''natronophilum'' Sorokin ''et al.'' 2015
====== Family ''[[Methanotrichaceae]]'' ======
Genus ''[[Methanothrix]]'' Huser ''et al.'' 1983
[[Methanothrix soehngenii|''Methanothrix'' ''soehngenii'']] Huser ''et al.'' 1983 (type species)
[[Methanothrix|''Methanothrix'' ''harundinacea'']] (Ma ''et al.'' 2006) Akinyemi ''et al.'' 2021
''Methanothrix'' ''thermoacetophila'' corrig. Nozhevnikova and Chudina 1988
"''Candidatus'' Methanothrix paradoxa" corrig. Angle ''et al.'' 2017
====== Family ''Methermicoccaceae'' ======
Genus ''Methermicoccus'' Cheng ''et al.'' 2007
[[Methermicoccus shengliensis|''Methermicoccus'' ''shengliensis'']] Cheng ''et al.'' 2007 (type species)
=== Phylum ''[[Methanobacteriota]]'' ===
==== '''Class ''[[Methanobacteria]]''''' ====
===== Order ''[[Methanobacteriales]]'' =====
====== Family ''[[Methanobacteriaceae]]'' ======
Genus ''[[Methanobacterium]]'' Kluyver and van Niel 1936
[[Methanobacterium formicicum|''Methanobacterium'' ''formicicum'']] Schnellen 1947 (type species)
''[[Methanobacterium bryantii]]''
Genus ''[[Methanobrevibacter]]'' Balch and Wolfe 1981
''[[Methanobrevibacter ruminantium]]'' (Smith and Hungate 1958) Balch and Wolfe 1981 (type species)
[[Methanobrevibacter acididurans|''Methanobrevibacter'' ''acididurans'']] Savant ''et al.'' 2002
''[[Methanobrevibacter arboriphilicus|Methanobrevibacter arboriphilus]]'' [[Methanobrevibacter arboriphilicus|corrig. (Zeikus and Henning 1975) Balch and Wolfe 1981]]
[[Methanobrevibacter|''Methanobrevibacter'' ''boviskoreani'']] Lee ''et al.'' 2013
[[Methanobrevibacter curvatus|''Methanobrevibacter'' ''curvatus'']] Leadbetter and Breznak 1997
[[Methanobrevibacter cuticularis|''Methanobrevibacter'' ''cuticularis'']] Leadbetter and Breznak 1997
[[Methanobrevibacter filiformis|''Methanobrevibacter'' ''filiformis'']] Leadbetter ''et al.'' 1998
[[Methanobrevibacter gottschalkii|''Methanobrevibacter'' ''gottschalkii'']] Miller and Lin 2002
[[Methanobrevibacter millerae|''Methanobrevibacter'' ''millerae'']] Rea ''et al.'' 2007
[[Methanobrevibacter olleyae|''Methanobrevibacter'' ''olleyae'']] Rea ''et al.'' 2007
[[Methanobrevibacter oralis|''Methanobrevibacter'' ''oralis'']] Ferrari ''et al.'' 1995
[[Methanobrevibacter smithii|''Methanobrevibacter'' ''smithii'']] Balch and Wolfe 1981
[[Methanobrevibacter thaueri|''Methanobrevibacter'' ''thaueri'']] Miller and Lin 2002
[[Methanobrevibacter woesei|''Methanobrevibacter'' ''woesei'']] Miller and Lin 2002
[[Methanobrevibacter wolinii|''Methanobrevibacter'' ''wolinii'']] Miller and Lin 2002
"''Methanobrevibacter'' ''massiliense''" Huynh ''et al.'' 2015
"''Candidatus'' Methanobrevibacter intestini" Chibani ''et al.'' 2022
Genus ''[[Methanosphaera]]'' Miller and Wolin 1985
[[Methanosphaera stadtmaniae|''Methanosphaera'' ''stadtmanae'']] corrig. Miller and Wolin 1985 (type species)
[[Methanosphaera cuniculi|''Methanosphaera'' ''cuniculi'']] Biavati ''et al.'' 1990
Genus ''[[Methanothermobacter]]'' Wasserfallen ''et al.'' 2000
''[[Methanothermobacter thermautotrophicus]]'' corrig. (Zeikus and Wolfe 1972) Wasserfallen et al. 2000 (type species)
''Methanothermobacter crinale'' Cheng et al. 2012
''[[Methanothermobacter defluvii]]'' (Kotelnikova et al. 1994) Boone 2002
[[Methanothermobacter marburgensis|''Methanothermobacter marburgensis'']] Wasserfallen et al. 2000
[[Methanothermobacter tenebrarum|''Methanothermobacter tenebrarum'']] Nakamura et al. 2013
''[[Methanothermobacter thermoflexus]]'' (Kotelnikova et al. 1994) Boone 2002
''[[Methanothermobacter thermophilus]]'' (Laurinavichus et al. 1990) Boone 2002
''[[Methanothermobacter wolfeii|Methanothermobacter wolfei]]'' corrig. (Winter et al. 1985) Wasserfallen et al. 2000
====== Family ''[[Methanothermaceae]]'' ======
Genus ''[[Methanothermus]]'' Stetter 1982
[[Methanothermus fervidus|''Methanothermus'' ''fervidus'']] Stetter 1982 (type species)
==== '''Class ''[[Methanopyri]]''''' ====
===== Order ''[[Methanopyrales]]'' =====
====== Family ''[[Methanopyraceae]]'' ======
Genus ''[[Methanopyrus]]'' Kurr ''et al.'' 1992
[[Methanopyrus kandleri|''Methanopyrus'' ''kandleri'']] Kurr ''et al.'' 1992 (type species)
==== '''Class ''[[Methanococci]]''''' ====
===== Order ''[[Methanococcales]]'' =====
====== Family ''[[Methanococcaceae]]'' Balch and Wolfe 1981 ======
Genus ''[[Methanococcus]]'' Kluyver and van Niel 1936
[[Methanococcus vannielii|''Methanococcus'' ''vannielii'']] Stadtman and Barker 1951 (type species)
''[[Methanococcus aeolicus]]''
''[[Methanococcus burtonii]]''
''[[Methanococcus chunghsingensis]]''
''[[Methanococcus deltae]]''
''[[Methanococcus jannaschii]]''
''[[Methanococcus maripaludis]]''
Genus ''[[Methanofervidicoccus]]''
[[Methanofervidicoccus abyssi|''Methanofervidicoccus'' ''abyssi'']] Sakai ''et al.'' 2019 (type species)
Genus ''[[Methanothermococcus]]''
[[Methanothermococcus thermolithotrophicus|''Methanothermococcus'' ''thermolithotrophicus'']] (Huber ''et al.'' 1984) Whitman 2002 (type species)
====== Family ''[[Methanocaldococcaceae]]'' ======
Genus ''[[Methanocaldococcus]]''
[[Methanocaldococcus jannaschii|''Methanocaldococcus'' ''jannaschii'']] (Jones ''et al.'' 1984) Whitman 2002 (type species)
Genus ''[[Methanotorris]]''
[[Methanotorris igneus|''Methanotorris'' ''igneus'']] (Burggraf ''et al.'' 1990) Whitman 2002 (type species)
=== Phylum ''[[Thermoplasmatota]]'' ===
==== Class ''[[Thermoplasmata]]'' ====
===== Order ''Methanomassiliicoccales'' =====
====== Family ''Methanomassiliicoccaceae'' ======
Genus ''Methanomassiliicoccus'' Dridi ''et al.'' 2012
[[Methanomassiliicoccus luminyensis|''Methanomassiliicoccus'' ''luminyensis'']] Dridi ''et al.'' 2012 (type species)
====== Family ''[[Methanomethylophilaceae]]'' ======
Genus ''[[Methanomethylophilus]]'' Borrel ''et al.'' 2024
[[Methanomethylophilus alvi|''Methanomethylophilus'' ''alvi'']] Borrel ''et al.'' 2024 (type species)
== See also ==
*[[Extremophile]]
*[[Hydrogen cycle]]
*[[List of Archaea genera]]
*[[Methane clathrate]]
*[[Methanogens in digestive tract of ruminants]]
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